Your libcgns.so seems not to be linked to hdf5 library.
ldd libcgns.so should be like this:
linux-vdso.so.1 (0x00007ffd0a3d4000)
libhdf5.so.10 =>
/home/yoshiaki/local/installed/lib/libhdf5.so.100x00007f5c52e94000)
libz.so.1 => /usr/lib64/libz.so.1 (0x00007f5c52c7d000)
libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f5c52a79000)
libm.so.6 => /usr/lib64/libm.so.6 (0x00007f5c52777000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00007f5c523b5000)
/lib64/ld-linux-x86-64.so.2 (0x000055f95909c000)
Did you set the following flags for CGNS installation? (I recommend you to
use cmake):
CGNS_ENABLE_HDF5 on
Then, path to HDF5 library should be specified:
HDF5_CXX_COMPILER_EXECUTABLE /usr/bin/h5c++
HDF5_C_COMPILER_EXECUTABLE /home/yoshiaki/local/installed/bin/h5cc
HDF5_C_INCLUDE_DIR /home/yoshiaki/local/installed/include
HDF5_DIFF_EXECUTABLE /home/yoshiaki/local/installed/bin/h5diff
HDF5_DIR HDF5_DIR-NOTFOUND
HDF5_Fortran_COMPILER_EXECUTAB /home/yoshiaki/local/installed/bin/h5fc
HDF5_hdf5_LIBRARY_RELEASE
/home/yoshiaki/local/installed/lib/libhdf5.so
I have installed HDF5 at /home/yoshiaki/local/installed.
I hope that this is helpful for you.
Regards,
Yoshiaki
On Friday, January 13, 2017 at 1:08:21 AM UTC, CatDog wrote:
>
> just found a permission problem, however, it seems irrelevant
>
> [root@localhost cgns_file]# ldd /usr/local/lib/libcgns.so
> ldd: warning: *you do not have execution permission* for
> `/usr/local/lib/libcgns.so'
> linux-vdso.so.1 => (0x00007ffea41fc000)
> libc.so.6 => /lib64/libc.so.6 (0x00007f7a8fbdc000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f7a90241000)
> [root@localhost cgns_file]# cd /usr/local/lib
> [root@localhost lib]# *chmod 755 libcgns.so*
> [root@localhost lib]# cd ~/cgns_file/
> [root@localhost cgns_file]# pyfr import -t cgns bump.cgns bump.pyfrm
> Traceback (most recent call last):
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/ctypesutil.py",
>
> line 22, in load_library
> File "/op/anaconda3/lib/python3.5/ctypes/__init__.py", line 347, in
> __init__
> self._handle = _dlopen(self._name, mode)
> OSError: /usr/local/lib/libcgns.so: undefined symbol: H5T_NATIVE_SCHAR_g
>
>
> During handling of the above exception, another exception occurred:
>
>
> Traceback (most recent call last):
> File "/op/anaconda3/bin/pyfr", line 11, in <module>
> load_entry_point('pyfr==1.5.0', 'console_scripts', 'pyfr')()
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py",
>
> line 110, in main
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py",
>
> line 118, in process_import
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/__init__.py",
>
> line 11, in get_reader_by_name
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/cgns.py",
>
> line 374, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/cgns.py",
>
> line 34, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/ctypesutil.py",
>
> line 31, in load_library
> OSError: Unable to load cgns
>
>
> On Thursday, January 12, 2017 at 10:24:47 PM UTC+8, CatDog wrote:
>>
>> I am running into some confusions about the CGNS lib.
>> The CGNS 3.3.0 is too much newer than my CentOS 6. So I have to compile
>> it with hdf5 (and szip, I am not sure if it is necessary). However, after
>> that, when I tried to import CGNS grid.
>>
>> wget http://cgns.sourceforge.net/CGNSFiles/Chris/bump.cgns.gz
>> gunzip bump.cgns.gz
>> pyfr import -t cgns bump.cgns bump.pyfrm
>>
>> I got this error:
>>
>> Traceback (most recent call last):
>> File
>> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/ctypesutil.py"
>> , line 22, in load_library
>> File "/op/anaconda3/lib/python3.5/ctypes/__init__.py", line 347, in
>> __init__
>> self._handle = _dlopen(self._name, mode)
>> OSError: /usr/local/lib/libcgns.so: undefined symbol: H5T_NATIVE_SCHAR_g
>>
>>
>> During handling of the above exception, another exception occurred:
>>
>>
>> Traceback (most recent call last):
>> File "/op/anaconda3/bin/pyfr", line 11, in <module>
>> load_entry_point('pyfr==1.5.0', 'console_scripts', 'pyfr')()
>> File
>> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py"
>> , line 110, in main
>> File
>> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py"
>> , line 118, in process_import
>> File
>> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/__init__.py"
>> , line 11, in get_reader_by_name
>> File
>> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/cgns.py"
>> , line 374, in __init__
>> File
>> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/cgns.py"
>> , line 34, in __init__
>> File
>> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/ctypesutil.py"
>> , line 31, in load_library
>> OSError: Unable to load cgns
>>
>> I googled "H5T_NATIVE_SCHAR_g", and I found the description at H5T:
>> Datatype Interface <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5T.html>.
>> It seems a fundamental part of hdf5.
>>
>> My compilation of CGNS is as follows:
>> #szip
>> wget https://
>> support.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz
>> tar xf szip-2.1.tar.gz
>> cd szip-2.1
>> ./configure --prefix=/usr/local
>> make
>> make install
>> cd
>>
>>
>> #hdf5
>> wget -b https://
>> support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.18.tar
>> tar xf hdf5-1.8.18.tar
>> cd hdf5-1.8.18
>> ./configure --prefix=/usr/local --enable-parallel --with-szlib
>> make
>> make install
>> cd
>>
>>
>> #CGNS
>> wget https://github.com/CGNS/CGNS/archive/v3.3.0.tar.gz
>> tar xf v3.3.0.tar.gz
>> cd CGNS-3.3.0/src
>> export FC=gfortran
>> export FCFLAGS=-fPIC
>> #"--with-hdf5=/usr/local" in order to avoid "-I" flag.
>> ./configure --prefix=/usr/local --with-mpi --with-szip --with-hdf5=/usr/
>> local --enable-64bit --enable-shared=all --enable-parallel
>> make
>> make install
>> cd
>>
>> I am using GCC 4.9.2 and CentOS 6 with OpenMPI
>> [root@localhost cgns_file]# mpicc --version
>> gcc (GCC) 4.9.2 20150212 (Red Hat 4.9.2-6)
>> Copyright (C) 2014 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions. There is
>> NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>> PURPOSE.
>>
>>
>> [root@localhost cgns_file]# uname -a
>> Linux localhost.localdomain 2.6.32-042stab120.11 #1 SMP Wed Nov 16
>> 12:05:45 MSK 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> [root@localhost cgns_file]# mpiexec --version
>> mpiexec (OpenRTE) 2.0.1
>>
>> Report bugs to http://www.open-mpi.org/community/help/
>>
>> Additionally, I want to know how important the threadsafety is to pyfr
>> when I need to use OpenMP? I found there is an threadsafety configure
>> option in HDF5 but I did not select it.
>>
>
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